Why does the color output change?
did you try to render a still image? If there is no problem with that I would suggest to always render animations just using still images, that has different advantages.

First, you can pause the render and continue at any point. 
Second there are just less possible problems, in my opinion. 
Third and most importantly, if something goes horribly wrong, for example your PC crashes, you do not have to start the render all over. 

The most preffered format for many is png, since it has a good balance between data size and quality loss, due to compression. 

Please comment, if this method is helpful, or not. :)